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I-TASSER results for job id Rv1325c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 Top 1 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)
 Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)


 Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)


  Ligand binding sites

Rank C-score Cluster
size
PDB
Hit
Lig
Name
Download
Complex
Ligand Binding Site Residues
10.14 8 4j78A III Rep, Mult 53,55,98,135,136,138,151,157,159,175,196,212,270
20.05 3 1e2rB UUU Rep, Mult 138,139,141,159,160,161,175,196,197,198,237,269,272
30.02 1 3a6zA CA Rep, Mult 405,406,407,408,410,423,424,425,428
40.02 1 1vq9B MG Rep, Mult 205,207
50.02 1 3huzP MG Rep, Mult 528,530
60.02 1 1n7dA UUU Rep, Mult 432,433
70.02 1 3iurA III Rep, Mult 313,325,326,327
80.02 1 1o0tA CA Rep, Mult 288,289,290,292,302,304,307
90.02 1 1go7P CA Rep, Mult 388,389,390,392,405,406,407,410
100.02 1 1af0A CA Rep, Mult 396,397,398,399,401,422
110.02 1 3pslA III Rep, Mult 53,54,55,94,97,98,114,136,138,238,270,286,288
120.02 1 1aofA UUU Rep, Mult 370,399,400,402,413,469,470,471
130.02 1 2z8xA CA Rep, Mult 495,497,499,506,507,508,511
140.02 1 3i7hA III Rep, Mult 54,56,71,136,160,197,235,236,237,271,285
150.02 1 4ewlB GOL Rep, Mult 197,198,201
160.02 1 1sqj0 III Rep, Mult 167,181,184,221,222,223,224,225
170.02 1 3odtA CA Rep, Mult 53,286,292
180.02 1 3shfA GBL Rep, Mult 361,362,399
190.02 1 3mj7A UUU Rep, Mult 506,509

Download the all possible binding ligands and detailed prediction summary.
Download the templates clustering results.
(a)C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)Cluster size is the total number of templates in a cluster.
(c)Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster.

  Enzyme Commission (EC) numbers and active sites

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0662ebsB0.6175.010.0780.7783.2.1.150NA
20.0601orvA0.3716.900.0300.5423.4.14.5NA
30.0601hn0A0.3617.610.0440.5764.2.2.20NA
40.0601aomB0.4183.920.0680.4811.7.99.1,1.7.2.1NA
50.0603c75J0.3554.560.0630.4311.4.99.3566
60.0601k32A0.5056.400.0530.7053.4.21.-NA
70.0601yr2A0.4247.550.0520.6633.4.21.2653,307
80.0601w6sC0.3535.080.0760.4431.1.99.8NA
90.0601g72A0.4233.470.0730.4811.1.99.8NA
100.0602gc7A0.3804.250.0690.4491.4.99.3462,475,520
110.0601z68A0.3765.290.0700.4883.4.21.-NA
120.0602madH0.3655.010.0870.4591.4.99.3440
130.0601bxrA0.3637.800.0450.5806.3.5.5NA
140.0601yrzA0.3666.220.0500.5043.2.1.37NA
150.0602gbcA0.3847.420.0540.5873.4.14.5,3.4.15.5NA
160.0602qr5A0.3936.390.0760.5573.4.19.1NA
170.0602ecfA0.3697.630.0470.5873.4.14.5NA
180.0603fsnB0.3675.630.0370.4885.2.1.7541
190.0601kv9A0.4253.300.0710.4791.1.99.-364
200.0601llwA0.3847.950.0600.6301.4.7.1NA

(a)CscoreEC is the confidence score for the EC number prediction. CscoreEC values range in between [0-1];
where a higher score indicates a more reliable EC number prediction.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided
by length of the query protein.

  Gene Ontology (GO) terms

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.090.6644.840.050.833j2tA GO:0000166 GO:0001666 GO:0001843 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0006919 GO:0007275 GO:0007399 GO:0007420 GO:0007568 GO:0007584 GO:0008635 GO:0008656 GO:0010659 GO:0030154 GO:0030900 GO:0031072 GO:0034349 GO:0042802 GO:0042981 GO:0043065 GO:0043293 GO:0043531 GO:0051260 GO:0051402 GO:0070059 GO:0070062 GO:0071560 GO:0072432 GO:0097190 GO:0097193 GO:1902510 GO:2001235
10.080.6465.590.060.863sfzA GO:0000166 GO:0001666 GO:0001843 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0006919 GO:0007275 GO:0007420 GO:0007568 GO:0007584 GO:0008635 GO:0008656 GO:0010659 GO:0030154 GO:0030900 GO:0031072 GO:0034349 GO:0042802 GO:0042981 GO:0043293 GO:0043531 GO:0051260 GO:0051402 GO:0070059 GO:0070062 GO:0071560 GO:0097190 GO:1902510 GO:2001235
20.070.6145.300.080.794nsxA GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030529 GO:0031167 GO:0032040 GO:0034388 GO:0042254 GO:0042274
30.070.5695.590.060.751nr0A GO:0003779 GO:0005737 GO:0005856 GO:0016528 GO:0030016 GO:0030240 GO:0030836 GO:0030837 GO:0040011 GO:0040012 GO:0042643 GO:0051015 GO:0071689
40.070.5845.490.050.774xfvA GO:0002098 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006810 GO:0008017 GO:0015031 GO:0032447 GO:0033588
50.070.5685.260.080.731pguB GO:0003779 GO:0005737 GO:0005856 GO:0005884 GO:0006970 GO:0030042 GO:0030479 GO:0032466 GO:0051016
60.070.5535.500.080.734ci8A GO:0000226 GO:0002244 GO:0005509 GO:0005737 GO:0005829 GO:0005856 GO:0005874 GO:0005875 GO:0007052 GO:0007405 GO:0007420 GO:0008017 GO:0015631 GO:0048471 GO:0097431 GO:1990023
70.070.5206.630.070.772ymuA GO:0016020 GO:0016021
80.060.4454.870.050.545cvlA GO:0000724 GO:0005634 GO:0005737 GO:0005764 GO:0005768 GO:0005770 GO:0006974 GO:0007283 GO:0007338 GO:0008584 GO:0016032 GO:0016579 GO:0035264 GO:0043588 GO:0048568 GO:0048705 GO:0048872 GO:0050679 GO:0072520 GO:1902525
90.060.4445.920.050.603mkqA GO:0005198 GO:0006886 GO:0016192 GO:0030117
100.060.4046.760.040.595a1vK GO:0000139 GO:0005179 GO:0005198 GO:0005576 GO:0005615 GO:0005737 GO:0005794 GO:0006810 GO:0006886 GO:0006888 GO:0006890 GO:0006891 GO:0015031 GO:0016020 GO:0016192 GO:0030117 GO:0030126 GO:0030157 GO:0030663 GO:0031410 GO:0070062
110.060.4266.700.040.615a1uD GO:0000139 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0006810 GO:0006886 GO:0006888 GO:0006890 GO:0006891 GO:0015031 GO:0016020 GO:0016192 GO:0030117 GO:0030126 GO:0030663 GO:0031410 GO:1901998
120.060.3654.700.070.453dm0A GO:0004871 GO:0005078 GO:0005215 GO:0005363 GO:0005634 GO:0005737 GO:0005829 GO:0006417 GO:0006810 GO:0006974 GO:0007165 GO:0008643 GO:0009507 GO:0009739 GO:0009749 GO:0009845 GO:0009967 GO:0010228 GO:0010476 GO:0015768 GO:0022626 GO:0030288 GO:0032947 GO:0034289 GO:0042254 GO:0042597 GO:0042956 GO:0043190 GO:0046686 GO:0055052 GO:0060326 GO:0071215 GO:1901982 GO:1990060
130.060.3363.710.040.384e54B GO:0000209 GO:0000715 GO:0000717 GO:0003677 GO:0003684 GO:0004842 GO:0005634 GO:0005654 GO:0006281 GO:0006289 GO:0006290 GO:0006293 GO:0006294 GO:0006295 GO:0006296 GO:0006974 GO:0009411 GO:0016567 GO:0030054 GO:0031465 GO:0033683 GO:0035518 GO:0043234 GO:0051865 GO:0070911 GO:0070914 GO:0080008
140.060.3653.810.040.432ce8A GO:0000122 GO:0001106 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0007165 GO:0007275 GO:0008134 GO:0009887 GO:0010628 GO:0016055 GO:0030178 GO:0042802 GO:0043124 GO:0045892 GO:1904837 GO:2000811
150.060.3343.210.040.374a11B GO:0000109 GO:0000209 GO:0003678 GO:0004842 GO:0005634 GO:0005654 GO:0006281 GO:0006283 GO:0006289 GO:0006974 GO:0006979 GO:0008094 GO:0009411 GO:0010165 GO:0016363 GO:0016567 GO:0031464 GO:0032403 GO:0043161 GO:0043234 GO:0045739 GO:0051865
160.060.3174.500.090.384v3pSa GO:0007165
170.060.3672.630.050.393jcrL GO:0000375 GO:0000398 GO:0005634 GO:0005654 GO:0005681 GO:0006396 GO:0006397 GO:0008380 GO:0015030 GO:0016607 GO:0017070 GO:0030621 GO:0046540 GO:0071001 GO:0097525
180.060.3673.760.070.434jxmA GO:0003723 GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030529 GO:0031428 GO:0032040 GO:0034511 GO:0044822


Consensus prediction of GO terms
 
Molecular Function GO:0032559 GO:0043028 GO:0035639 GO:0005515 GO:0032550 GO:0016505
GO-Score 0.33 0.33 0.33 0.33 0.33 0.33
Biological Processes GO:0071495 GO:0051128 GO:0071363 GO:0034976 GO:1903624 GO:0097193 GO:0043280 GO:0060322 GO:0014020 GO:0070997 GO:0060606 GO:0048513 GO:2001233 GO:0010658 GO:0031667 GO:0007417 GO:0051259 GO:0071559 GO:0036293 GO:0006309 GO:0048869 GO:0009967 GO:1900117
GO-Score 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33
Cellular Component GO:0043231 GO:0031988 GO:0044445 GO:0043234 GO:1903561
GO-Score 0.55 0.33 0.33 0.33 0.33

(a)CscoreGO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on CscoreGO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]



Please cite the following articles when you use the I-TASSER server:
1. J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2. J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.